RE: [PyMOL] conformational states in the mutagenesis wizard
Xavier, PyMOL 0.99beta09 and earlier use a crude backbone-independent rotamer library. However, current development versions (PyMOL 0.99beta10 on up) now provide both the Dunbrack backbone-dependent and backbone-independent rotamers. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Xavier Deupi > Sent: Friday, August 12, 2005 2:34 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] conformational states in the mutagenesis wizard > > Hi, > > I've just realized that through the mutagenesis wizard you > can view/select different conformations for a sidechain. I've > been playing around, and it seems that the conformations are > selected according to a backbone-independent rotamer library. > Am I correct? Which library has been used? > > I would also like to know if there is anybody out there using > the rotamer toggle plugin. I've just installed it, and > although it seems extremely useful, it makes PyMOL very slow > to start. I'm running PyMOL > 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM > (running MacOS X > 10.4.2) > > Thanks in advance, > > Xavier > > -- > Xavier Deupi, Ph.D. > Department of Molecular and Cellular Physiology Beckman > Center for Molecular and Genetic Medicine (B161) > 279 Campus Drive, Stanford University School of Medicine > Stanford, CA 94305 (USA) > > E-mail: xavier.de...@stanford.edu > Phone: +1 (650) 725-6497 > Fax : +1 (650) 725-8021 > > > > --- > SF.Net email is Sponsored by the Better Software Conference & > EXPO September 19-22, 2005 * San Francisco, CA * Development > Lifecycle Practices Agile & Plan-Driven Development * > Managing Projects & Teams * Testing & QA Security * Process > Improvement & Measurement * http://www.sqe.com/bsce5sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
Re: [PyMOL] Shadows
Hi Corinne, Sabuj, You're right with regards to the CGO. An example script (written by Gareth Stockwell) can be found at http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the raytracing, don't be fooled, I'd say this was Pymol's internal raytracer :) Hope it helps, Tsjerk On 8/12/05, Sabuj Pattanayek wrote: > It looks like a CGO (compiled graphics object) behind the molecule, then > rendered using pov-ray, probably a script floating around to do this > somewhere on the internets. > > Corinne Zeitler wrote: > > Hi, > > > > I was wondering if anyone knows how to produce the type of image in > > Pymol that is on the Pymol Galleray page > > (http://pymol.sourceforge.net/pmimag.html). I would like to know > > specifically how to make the shadow of the molecule appear in the > > background. Thank you! > > > > Corinne Zeitler > > Graduate Student > > Baylor College of Medicine > > > > --- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?
I use a cheap microsoft optical (or basic optical) usb mouse on linux, so it should work on your macosx. If you want something more configurable under macosx and don't want to destroy the "Appleness" of your computer with an MS mouse then this might work for you http://www.apple.com/mightymouse/ . I hear there will be a wireless version soon. Sarina Bromberg wrote: I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- button mouse, but I can never get it to produce the results provided for 3-button viewing or editing by PyMOL. Perhaps I do not have it configured correctly (I cannot find a clue in the instructions or in simple experiments), or perhaps this is not the kind of 3-button mouse I need. Does anyone have a good solution? Tx, Sarina Bromberg --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Shadows
It looks like a CGO (compiled graphics object) behind the molecule, then rendered using pov-ray, probably a script floating around to do this somewhere on the internets. Corinne Zeitler wrote: Hi, I was wondering if anyone knows how to produce the type of image in Pymol that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.html). I would like to know specifically how to make the shadow of the molecule appear in the background. Thank you! Corinne Zeitler Graduate Student Baylor College of Medicine
[PyMOL] conformational states in the mutagenesis wizard
Hi, I've just realized that through the mutagenesis wizard you can view/select different conformations for a sidechain. I've been playing around, and it seems that the conformations are selected according to a backbone-independent rotamer library. Am I correct? Which library has been used? I would also like to know if there is anybody out there using the rotamer toggle plugin. I've just installed it, and although it seems extremely useful, it makes PyMOL very slow to start. I'm running PyMOL 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM (running MacOS X 10.4.2) Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: xavier.de...@stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021
Re: [PyMOL] comments ?
Hi I have installed version 0.98 on my new dual processor machine running windows XP. Pymol runs fine, but when trying to load a large PDB file (~4Mb), the program crashes and I get a runtime error: "This application has requested the Runtime to terminate it in an unusual way" Does anyone have some advice? Thanks, Michael Michael S. Cosgrove, Ph.D. Assistant Professor Syracuse University Department of Biology 406D Lyman Hall 108 College Place Syracuse, NY 13244 Phone: (315) 443-2964 Fax: (315) 443-2156 Email: mscos...@syr.edu
RE: [PyMOL] Newline character in scene annotation message
Carsten,
Hmm...
Unfortunately, the PyMOL command language currently provide any way of
expressing a newline character, so you will need to use the API form of
the scene command. Note that it is perfectly legal to use that form in
a ".pml" file as follows, without an intervening variable:
cmd.scene("new","store","line1\nline2")
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Schubert, Carsten [PRDUS]
> Sent: Friday, August 12, 2005 12:57 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Newline character in scene annotation message
>
> Hi
>
> I am trying to combine a scene with annotations spanning
> several lines.
> So far something like
> > scene new, store, message="Line1\nLine2"
>
> would produce some nice coloration effects but not a newline
> character.
>
> I was able to use the api function to do the trick
> >mesg="line1\nline2"
> >cmd.scene("new","store",message=mesg)
>
> but I was wondering is there a way to use the non API
> function in the same way?
>
> Thanks
>
> Carsten
>
>
[PyMOL] Newline character in scene annotation message
Hi
I am trying to combine a scene with annotations spanning several lines.
So far something like
> scene new, store, message="Line1\nLine2"
would produce some nice coloration effects but not a newline character.
I was able to use the api function to do the trick
>mesg="line1\nline2"
>cmd.scene("new","store",message=mesg)
but I was wondering is there a way to use the non API function in the same
way?
Thanks
Carsten
[PyMOL] Shadows
Hi, I was wondering if anyone knows how to produce the type of image in Pymol that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.html). I would like to know specifically how to make the shadow of the molecule appear in the background. Thank you! Corinne Zeitler Graduate Student Baylor College of Medicine
RE: [PyMOL] Saving a carved section of a map.
Hi Carsten, This isn't yet possible from within PyMOL, but it will be soon since it is a recurring request. In the meantime unforutnately, you will need to truncate the maps outside of PyMOL in order to generate smaller session files. Sorry about that! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Schubert, Carsten [PRDUS] > Sent: Friday, August 12, 2005 11:56 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Saving a carved section of a map. > > Hi > > I was wondering if it is possible to save a carved out > section of a map and the read it back into pymol as a > separate map. The background is that I'd like to distribute > .psw files with a couple of maps, but they get rather large > (>50 MB) since the map data is not compressed in pymol. I am > only interested in a small portion of the map centered around > a ligand and some residues, so the rest of the map would be > unnecessary since it will not be shown anyway. > > I have tried if mapman could do the trick but apparently not. > I could probably restrict the calculation of the map to be > only centered around a region of interest, but was wondering > if this would be possible in pymol. > > > Thanks > > Carsten > >
[PyMOL] Saving a carved section of a map.
Hi I was wondering if it is possible to save a carved out section of a map and the read it back into pymol as a separate map. The background is that I'd like to distribute .psw files with a couple of maps, but they get rather large (>50 MB) since the map data is not compressed in pymol. I am only interested in a small portion of the map centered around a ligand and some residues, so the rest of the map would be unnecessary since it will not be shown anyway. I have tried if mapman could do the trick but apparently not. I could probably restrict the calculation of the map to be only centered around a region of interest, but was wondering if this would be possible in pymol. Thanks Carsten
[PyMOL] What is the best 3 button mouse for PyMOL on a Mac OSX?
I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- button mouse, but I can never get it to produce the results provided for 3-button viewing or editing by PyMOL. Perhaps I do not have it configured correctly (I cannot find a clue in the instructions or in simple experiments), or perhaps this is not the kind of 3-button mouse I need. Does anyone have a good solution? Tx, Sarina Bromberg
[PyMOL] PML files
Hi, does anyone know what file type to save text as (in OS X) for a .pml file? I can't get PyMol to recognize RTF, etc... thanks Avram Slovic
Re: [PyMOL] Setting transparency for CGOs
Hi, I've done this by rendering two images (actually 4 to get stereo). One without the CGOs and one with them. Then I overlaid them with photoshop and changed the trasnparency of the CGO containing layer. I just used triangles and it looked rather nice. ~Lari~ ___ Lari Lehtiö University of Helsinki Institute of Biotechnology Macromolecular X-ray crystallography P.O.Box 65 00014 HY Finland http://www.biocenter.helsinki.fi/~lehtio/ ___ Quoting tanri...@stud.uni-frankfurt.de: # Hi everybody, # # i've just created many CGOs, which show up solid surfaces like spheres and # ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 # and leave the others solid? # I've checked out the reference and the manual, and found something like: # # set transparency=0.5, object # # But this actually does not work for CGO's. # Any ideas # # Yusuf # # # -- # Yusuf Tanrikulu # Bioinformatics Diploma Student # Department of Biosciences # Johann-Wolfgang-Goethe Univerity Frankfurt # Siesmayerstrasse 70 # 60326 Frankfurt am Main # - Germany - # tanrik...@bioinformatik.uni-frankfurt.de # # # --- # SF.Net email is Sponsored by the Better Software Conference & EXPO # September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices # Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA # Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf # ___ # PyMOL-users mailing list # PyMOL-users@lists.sourceforge.net # https://lists.sourceforge.net/lists/listinfo/pymol-users #
[PyMOL] Setting transparency for CGOs
Hi everybody, i've just created many CGOs, which show up solid surfaces like spheres and ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 and leave the others solid? I've checked out the reference and the manual, and found something like: set transparency=0.5, object But this actually does not work for CGO's. Any ideas Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesmayerstrasse 70 60326 Frankfurt am Main - Germany - tanrik...@bioinformatik.uni-frankfurt.de
